They are a lone hero's best defence against a villain. To illustrate this, I will take a case in point, The Matrix. The hero, Neo, skills are shown being developed over the course of the film. First, Neo is a nobody, just a computer geek with a 'splinter' in his mind; however he is still marked as the hero, so that Morpheus, when he finds Neo, knows that all Neo has to do to become "the one" is develop his potential. This potential is articulated in Neo's special skills.

The first special skills Neo aquires are, naturally, physical ones. This is shown in the dojo scene, where he must test out his newly aquired martial arts prowess against Morpheus. But the rest of the film's development focuses on whether Neo will fully become the hero. When he does so, he aquires the special skill to alter the matrix at will (If I am correct). The turning point comes in his development when Neo decides to attempt the rescue of Morpheus, which fellow freedom fighter Trinity tells him is impossible.

However, Neo does succeed in rescuing Morpheus, and manages to come back from the dead in the process (if that ain't a hell of a special skill, I don't know what is). At this point, Neo has fully realized his development into a hero, and "the one", by realizing his specical skills. -This is whats special about special skills; they give the hero the ability to do what no other can do. To fight the overwhelming power that their adversary may hold, and prevail, through some miracle, against impossible odds.

These skills are part of what make ever hero unique in their own way, and what allow the hero to pursue justice while others are helpless. For reference, see the idea of lone hero persuing justice.

Having further considered this, I have decided that villain may possess some of the same special skills as the hero posesses. The hero uses these skills for good, and naturally is able to defeat villains, because good always defeats evil.